Add CNIC loader from custom branch of Arbor @drosophilia

CMakeLists.txt

@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 3.27)
 find_package(Git)
 
 project(the-arbor-gui
-  VERSION 0.11.1
+  VERSION 0.11.2
   LANGUAGES C CXX)
 
 set(EXPORT_COMPILE_COMMANDS ON)
@@ -186,22 +186,53 @@ if(ARBORGUI_BUILD_BUNDLE)
 
     set(ARBORGUI_ICON arbor.icns)
     set(ARBORGUI_ICON_PATH ${CMAKE_SOURCE_DIR}/images/${ARBORGUI_ICON})
-    set_source_files_properties(${ARBORGUI_ICON} PROPERTIES MACOSX_PACKAGE_LOCATION Resources)
 
-    add_executable(arbor-gui MACOSX_BUNDLE ${ARBORGUI_ICON_PATH} ${gui_srcs} $<TARGET_OBJECTS:imgui>)
-    set_target_properties(arbor-gui PROPERTIES MACOSX_BUNDLE_ICONFILE ${ARBORGUI_ICON})
+    set(arbgui_resources)
+    set_source_files_properties(${CMAKE_SOURCE_DIR}/imgui.ini
+                                PROPERTIES
+                                    MACOSX_PACKAGE_LOCATION Resources)
+    list(APPEND arbgui_resources ${CMAKE_SOURCE_DIR}/imgui.ini)
+
+    file(GLOB_RECURSE shaders ${CMAKE_SOURCE_DIR}/glsl/*/*.glsl)
+    foreach(SHADER_FILE ${shaders})
+      list(APPEND arbgui_resources ${SHADER_FILE})
+      file(RELATIVE_PATH SHADER_REL ${CMAKE_SOURCE_DIR}/glsl ${SHADER_FILE})
+      get_filename_component(SHADER_DIR ${SHADER_REL} DIRECTORY)
+      set_source_files_properties(${SHADER_FILE}
+                                  PROPERTIES
+                                      MACOSX_PACKAGE_LOCATION Resources/glsl/${SHADER_DIR})
+    endforeach()
+
+    file(GLOB_RECURSE fonts ${CMAKE_SOURCE_DIR}/fonts/*/*.ttf)
+    foreach(FONT_FILE ${fonts})
+      list(APPEND arbgui_resources ${FONT_FILE})
+      file(RELATIVE_PATH FONT_REL ${CMAKE_SOURCE_DIR}/fonts ${FONT_FILE})
+      get_filename_component(FONT_DIR ${FONT_REL} DIRECTORY)
+      set_source_files_properties(${FONT_FILE}
+                                  PROPERTIES
+                                      MACOSX_PACKAGE_LOCATION Resources/fonts/${FONT_DIR})
+    endforeach()
+
+    set_source_files_properties(${CMAKE_SOURCE_DIR}/images/arbor.icns
+                                PROPERTIES
+                                    MACOSX_PACKAGE_LOCATION Resources)
+
+    add_executable(arbor-gui MACOSX_BUNDLE ${gui_srcs} $<TARGET_OBJECTS:imgui> ${arbgui_resources} ${CMAKE_SOURCE_DIR}/images/arbor.icns)
+    set_target_properties(arbor-gui
+                          PROPERTIES
+                              BUNDLE True
+                              MACOSX_BUNDLE_BUNDLE_NAME ${PROJECT_NAME}
+                              MACOSX_BUNDLE_BUNDLE_VERSION ${PROJECT_VERSION}
+                              MACOSX_BUNDLE_ICONFILE ${ARBORGUI_ICON}
+                              MACOSX_BUNDLE_INFO_STRING "A GUI for Arbor"
+                              RESOURCE ${arbgui_resources})
     target_compile_definitions(arbor-gui PUBLIC FMT_HEADER_ONLY)
     target_include_directories(arbor-gui PRIVATE src ${CMAKE_CURRENT_BINARY_DIR})
     target_link_libraries(arbor-gui PRIVATE ${ARBORGUI_LIBS} arbor arborio glbinding glfw arbor-gui-deps)
 
     install(TARGETS arbor-gui
-        BUNDLE DESTINATION . COMPONENT Runtime
-        RUNTIME DESTINATION bin COMPONENT Runtime)
-
-    install(FILES     ${ARBORGUI_ICON_PATH} DESTINATION ${resource_path})
-    install(FILES     default.ini           DESTINATION ${resource_path} RENAME imgui.ini)
-    install(DIRECTORY glsl                  DESTINATION ${resource_path})
-    install(DIRECTORY fonts                 DESTINATION ${resource_path})
+            BUNDLE DESTINATION . COMPONENT Runtime
+            RUNTIME DESTINATION bin COMPONENT Runtime)
 
     set(CPACK_BINARY_DRAGNDROP ON)
     set(CPACK_GENERATOR "DragNDrop")
@@ -237,7 +268,7 @@ else()
   endif()
 
   # install resources
-  install(DIRECTORY glsl    DESTINATION ${resource_path})
-  install(DIRECTORY fonts   DESTINATION ${resource_path})
-  install(FILES default.ini DESTINATION ${resource_path} RENAME imgui.ini)
+  install(DIRECTORY glsl      DESTINATION ${resource_path})
+  install(DIRECTORY fonts     DESTINATION ${resource_path})
+  install(FILES     imgui.ini DESTINATION ${resource_path})
 endif()

src/loader.cpp

@@ -23,14 +23,33 @@ loaded_morphology load_swc(const std::filesystem::path &fn,
 }
 
 loaded_morphology load_neuron_swc(const std::filesystem::path &fn) {
-    auto loaded = arborio::load_swc_neuron(fn);
+    arborio::swc_loader_options opts;
+    auto loaded = arborio::load_swc_neuron(fn, opts);
     loaded_morphology res{.morph=loaded.morphology};
     for (const auto& [k, v]: loaded.labels.regions()) res.regions.emplace_back(k, to_string(v));
     for (const auto& [k, v]: loaded.labels.locsets()) res.locsets.emplace_back(k, to_string(v));
     log_info("Loaded SWC (Neuron) {} branches {} ", loaded.segment_tree.size(), loaded.morphology.num_branches());
     return res;
 }
 
+loaded_morphology load_cnic_swc(const std::filesystem::path &fn) {
+    arborio::swc_loader_options opts {.allow_non_monotonic_ids=true,
+                                      .allow_mismatched_tags=true,
+                                      .tags={{0, "undefined"},
+                                             {1, "soma"}, {2, "axon"}, {3, "dend"}, {4, "apic"},
+                                             {5, "fork point"},
+                                             {6, "end point"}}
+   };
+
+    auto loaded = arborio::load_swc_neuron(fn, opts);
+    loaded_morphology res{.morph=loaded.morphology};
+    for (const auto& [k, v]: loaded.labels.regions()) res.regions.emplace_back(k, to_string(v));
+    for (const auto& [k, v]: loaded.labels.locsets()) res.locsets.emplace_back(k, to_string(v));
+    log_info("Loaded SWC (Neuron) {} branches {} ", loaded.segment_tree.size(), loaded.morphology.num_branches());
+    return res;
+}
+
+
 loaded_morphology load_arbor_swc(const std::filesystem::path &fn) {
     auto loaded = arborio::load_swc_arbor(fn);
     loaded_morphology res{.morph=loaded.morphology};
@@ -78,7 +97,8 @@ static std::unordered_map<std::string,
                           std::unordered_map<std::string,
                                              std::function<loaded_morphology(const std::filesystem::path &fn)>>>
 loaders{{".swc", {{"Arbor",   load_arbor_swc},
-                  {"Neuron",  load_neuron_swc}}},
+                  {"Neuron",  load_neuron_swc},
+                  {"CNIC",    load_cnic_swc}}},
         {".nml", {{"Cell",    load_neuroml_cell},
                   {"Morph",   load_neuroml_morph}}},
         {".asc", {{"Default", load_asc}}}};

src/utils.cpp

@@ -21,7 +21,7 @@ std::filesystem::path get_resource_path(const std::filesystem::path& fn) {
   CFURLRef appUrlRef = CFBundleCopyBundleURL( CFBundleGetMainBundle() );
   CFStringRef macPath = CFURLCopyFileSystemPath( appUrlRef, kCFURLPOSIXPathStyle );
   CFStringEncoding encodingMethod = CFStringGetSystemEncoding();
-  const char* path = CFStringGetCStringPtr(macPath, encodingMethod);
+  auto path = std::string(CFStringGetCStringPtr(macPath, encodingMethod));
   CFRelease(appUrlRef);
   CFRelease(macPath);
   return std::filesystem::path{path} / "Contents/Resources" / fn;